Toward an Automatic Determination of Enzymatic Reaction Mechanisms and Their Activation Free Energies
comunitat-uji-handle:10234/9
comunitat-uji-handle2:10234/7013
comunitat-uji-handle3:10234/8638
comunitat-uji-handle4:
INVESTIGACIONAquest recurs és restringit
http://dx.doi.org/ 10.1021/ct400153r |
Metadades
Títol
Toward an Automatic Determination of Enzymatic Reaction Mechanisms and Their Activation Free EnergiesData de publicació
2013Editor
American Chemical SocietyISSN
1549-9618Cita bibliogràfica
ZINOVJEV, Kirill; RUIZ-PERNÍA, J. Javier; TUÑÓN, Iñaki. Toward an automatic determination of enzymatic reaction mechanisms and their activation free energies. Journal of Chemical Theory and Computation, 2013, 9.8: 3740-3749.Tipus de document
info:eu-repo/semantics/articleVersió de l'editorial
http://pubs.acs.org/doi/abs/10.1021/ct400153rVersió
info:eu-repo/semantics/publishedVersionParaules clau / Matèries
Resum
We present a combination of the string method and a path collective variable for the exploration of the free energy surface associated to a chemical reaction in condensed environments. The on-the-fly string method is ... [+]
We present a combination of the string method and a path collective variable for the exploration of the free energy surface associated to a chemical reaction in condensed environments. The on-the-fly string method is employed to find the minimum free energy paths on a multidimensional free energy surface defined in terms of interatomic distances, which is a convenient selection to study bond forming/breaking processes. Once the paths have been determined, a reaction coordinate is defined as a measure of the advance of the system along these paths. This reaction coordinate can be then used to trace the reaction Potential of Mean Force from which the activation free energy can be obtained. This combination of methodologies has been here applied to the study, by means of Quantum Mechanics/Molecular Mechanics simulations, of the reaction catalyzed by guanidinoacetate methyltransferase. This enzyme catalyzes the methylation of guanidinoacetate by S-adenosyl-l-methionine, a reaction that involves a methyl transfer and a proton transfer and for which different reaction mechanisms have been proposed. [-]
Publicat a
Journal of Chemical Theory and Computation, 2013, 9.8Drets d'accés
Copyright © 2013 American Chemical Society
http://rightsstatements.org/vocab/InC/1.0/
info:eu-repo/semantics/restrictedAccess
http://rightsstatements.org/vocab/InC/1.0/
info:eu-repo/semantics/restrictedAccess
Apareix a les col.leccions
- QFA_Articles [826]